+Open data
-Basic information
Entry | Database: PDB / ID: 6j8w | ||||||
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Title | Structure of MOEN5-SSO7D fusion protein in complex with lig 1 | ||||||
Components | MoeN5,DNA-binding protein 7d | ||||||
Keywords | TRANSFERASE / MOENOMYCIN / ANTIBIOTICS / BIOSYNTHESIS / PRENYL TRANSFERASE / ALPHA | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces ghanaensis (bacteria) Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Ko, T.P. / Zhang, L.L. / Chen, C.C. / Guo, R.T. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2019 Title: Complex structures of MoeN5 with substrate analogues suggest sequential catalytic mechanism. Authors: Zhang, L.L. / Ko, T.P. / Malwal, S.R. / Liu, W.D. / Zhou, S.Y. / Yu, X.J. / Oldfield, E. / Guo, R.T. / Chen, C.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j8w.cif.gz | 243.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j8w.ent.gz | 194 KB | Display | PDB format |
PDBx/mmJSON format | 6j8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j8w_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6j8w_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6j8w_validation.xml.gz | 47.1 KB | Display | |
Data in CIF | 6j8w_validation.cif.gz | 67.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/6j8w ftp://data.pdbj.org/pub/pdb/validation_reports/j8/6j8w | HTTPS FTP |
-Related structure data
Related structure data | 5gwvC 5gwwC 6j8vC 5b02S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37581.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: MOEN5-SSO7D fusion protein Source: (gene. exp.) Streptomyces ghanaensis (bacteria), (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea) Gene: moeN5, sso7d, sso7d-1, SSO10610 / Plasmid: pET32Xa/LIC / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A010, UniProt: P39476 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.76 % / Mosaicity: 0.748 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.1 / Details: 0.2M LI3-CITRATE, 0.3M NACL, 25% W/V PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 23, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.34→25 Å / Num. obs: 65630 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.039 / Rrim(I) all: 0.103 / Χ2: 1.419 / Net I/σ(I): 10.9 / Num. measured all: 461075 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B02 Resolution: 2.35→25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.027 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.58 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→25 Å
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Refine LS restraints |
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